dbSNP rs4784549: LPCAT2:c.1315-103T>A (chr16-55579006-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017839.5(LPCAT2):c.1315-103T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 1,053,600 control chromosomes in the GnomAD database, including 165,492 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 29231 hom., cov: 32)

Exomes 𝑓: 0.54 ( 136261 hom. )

Consequence

LPCAT2
NM_017839.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.70

Publications

10 publications found

Variant links:

Genes affected

LPCAT2 (HGNC:26032): (lysophosphatidylcholine acyltransferase 2) This gene encodes a member of the lysophospholipid acyltransferase family. The encoded enzyme may function in two ways: to catalyze the biosynthesis of platelet-activating factor (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) from 1-O-alkyl-sn-glycero-3-phosphocholine, and to catalyze the synthesis of glycerophospholipid precursors from arachidonyl-CoA and lysophosphatidylcholine. The encoded protein may function in membrane biogenesis and production of platelet-activating factor in inflammatory cells. The enzyme may localize to the endoplasmic reticulum and the Golgi. [provided by RefSeq, Feb 2009]

LPCAT2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017839.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPCAT2	NM_017839.5	MANE Select	c.1315-103T>A		intron	N/A	NP_060309.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LPCAT2	ENST00000262134.10	TSL:1 MANE Select	c.1315-103T>A	intron	N/A	ENSP00000262134.5	Q7L5N7-1
LPCAT2	ENST00000566915.5	TSL:1	n.1397-103T>A	intron	N/A
LPCAT2	ENST00000947554.1		c.1336-103T>A	intron	N/A	ENSP00000617613.1

Frequencies

GnomAD3 genomes

AF:

0.606

AC:

92111

AN:

152002

Hom.:

29194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.793

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.545

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.736

Gnomad SAS

AF:

0.710

Gnomad FIN

AF:

0.519

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.513

Gnomad OTH

AF:

0.584

GnomAD4 exome

AF:

0.543

AC:

489942

AN:

901480

Hom.:

136261

Cov.:

AF XY:

0.547

AC XY:

253023

AN XY:

462238

show subpopulations

African (AFR)

AF:

0.805

AC:

17156

AN:

21300

American (AMR)

AF:

0.559

AC:

18026

AN:

32244

Ashkenazi Jewish (ASJ)

AF:

0.488

AC:

8689

AN:

17814

East Asian (EAS)

AF:

0.719

AC:

26479

AN:

36814

South Asian (SAS)

AF:

0.687

AC:

42431

AN:

61784

European-Finnish (FIN)

AF:

0.521

AC:

24804

AN:

47578

Middle Eastern (MID)

AF:

0.579

AC:

1686

AN:

2912

European-Non Finnish (NFE)

AF:

0.512

AC:

327802

AN:

640146

Other (OTH)

AF:

0.559

AC:

22869

AN:

40888

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

10784

21568

32352

43136

53920

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7690

15380

23070

30760

38450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.606

AC:

92203

AN:

152120

Hom.:

29231

Cov.:

AF XY:

0.609

AC XY:

45302

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.793

AC:

32929

AN:

41524

American (AMR)

AF:

0.545

AC:

8317

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

1680

AN:

3468

East Asian (EAS)

AF:

0.736

AC:

3804

AN:

5170

South Asian (SAS)

AF:

0.710

AC:

3428

AN:

4826

European-Finnish (FIN)

AF:

0.519

AC:

5487

AN:

10574

Middle Eastern (MID)

AF:

0.612

AC:

180

AN:

294

European-Non Finnish (NFE)

AF:

0.513

AC:

34865

AN:

67980

Other (OTH)

AF:

0.589

AC:

1245

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1747

3493

5240

6986

8733

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

756

1512

2268

3024

3780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.559

Hom.:

3019

Bravo

AF:

0.614

Asia WGS

AF:

0.775

AC:

2698

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.045

(source)

DANN

Benign

0.55

PhyloP100

-2.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over